SNP Report

Basic Info

Name	rs2812393 dbSNP Ensembl
Location	chr1:231777927 - 231777927(1)
Variant Alleles	G/C
Ancestral Allele	C
Minor Allele	G
Minor Allele Frequence	0.378594
Functional Annotation	intron_variant; NMD_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000295051, ENST00000366632, ENST00000366633, ENST00000366636, ENST00000366637, ENST00000422590, ENST00000439617, ENST00000535944, ENST00000535983, ENST00000537876, ENST00000539444, ENST00000602281, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602873, ENST00000602885, ENST00000602956, ENST00000602962, ENST00000620189, ENST00000622252, ENST00000628350); NMD_transcript_variant(ENST00000295051, ENST00000366632, ENST00000422590, ENST00000535944, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602885, ENST00000602956, ENST00000602962)
No. of Studies	3 (Positive: 1; Negative: 2; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Ram Murthy, A., 2012		BPAD patients: P-value=0.135, P-value=0.122 for females, P-v...... BPAD patients: P-value=0.135, P-value=0.122 for females, P-value=0.532 for males; BPAD&SCZ: P-value=0.073, P-value=0.028 for females, P-value=0.668 for males More...	Moderate associations were also observed in females for rs28...... Moderate associations were also observed in females for rs2812393 (SCZ, P=0.026; BPAD&SCZ, P=0.028). More...	Positive
Thomson, P. A.,2005(a)		Single-Marker Analysis: allele frequency, for BP, P-value = ...... Single-Marker Analysis: allele frequency, for BP, P-value = 0.73 More...	No significant association was observed. No significant association was observed.	Negative
Yosifova, A.,2009	C/G	Allelic association: P-value = 0.78 Allelic association: P-value = 0.78	No significant association was observed No significant association was observed	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
TSNAX	translin-associated factor X	1q42.2	4(3/1/0)
DISC1	disrupted in schizophrenia 1	1q42.1	18(10/7/1)

SNPs in LD with rs2812393 (count: 3) View in gBrowse (chr1:231775265..231777927 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs2812390	intron_variant; NMD_transcript_variant	0.959[CEU]
rs2812389	intron_variant; NMD_transcript_variant	0.821[CEU]; 0.858[TSI]
rs2812392	intron_variant; NMD_transcript_variant	0.961[CEU]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Ram Murthy, A., 2012	SZ patients: P-value=0.093, P-value=0.026 for females, P-value=0.775 for males; BPAD&SCZ: P-value=0.073, P-value=0.028 for females, P-value=0.668 for males	Moderate associations were also observed in females for rs2812393 (SCZ, P=0.026; BPAD&SCZ, P=0.028).	Positive
Thomson, P. A.,2005(a)	Single-Marker Analysis:allele frequency, for SZ, P-value = 0.6	No significant association was observed.	Negative

Overlap with MDD from cross-disorder studies (count: 0)